Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression

2018 ◽  
Vol 56 (1) ◽  
pp. 1-20 ◽  
Author(s):  
Giuliano Bonanomi ◽  
Matteo Lorito ◽  
Francesco Vinale ◽  
Sheridan L. Woo
Keyword(s):  
Plant Pathogens ◽  
Management Practices ◽  
Organic Amendments ◽  
Crop Productivity ◽  
Disease Suppression ◽  
Biocontrol Agents ◽  
Unified Framework ◽  
Soil Microbiota ◽  
Beneficial Microbes

Organic amendments (OAs) and soilborne biocontrol agents or beneficial microbes (BMs) have been extensively studied and applied worldwide in most agriculturally important plant species. However, poor integration of research and technical approaches has limited the development of effective disease management practices based on the combination of these two bio-based strategies. Insights into the importance of the plant-associated microbiome for crop productivity, which can be modified or modulated by introducing OAs and/or BMs, are providing novel opportunities to achieve the goal of long-term disease control. This review discusses novel ways of functionally characterizing OAs and how they may be used to promote the effect of added biocontrol agents and/or beneficial soil microbiota to support natural suppressiveness of plant pathogens.

scholarly journals Microbiota Management for Effective Disease Suppression: A Systematic Comparison between Soil and Mammals Gut

2021 ◽  
Vol 13 (14) ◽  
pp. 7608
Author(s):  
Giuliano Bonanomi ◽  
Mohamed Idbella ◽  
Ahmed M. Abd-ElGawad
Keyword(s):  
Diet Composition ◽  
Management Practices ◽  
Organic Amendment ◽  
Soil Health ◽  
Organic Amendments ◽  
Crop Productivity ◽  
Disease Suppression ◽  
Functional Link ◽  
Harmful Organisms ◽  
Ecological Mechanisms

Both soil and the human gut support vast microbial biodiversity, in which the microbiota plays critical roles in regulating harmful organisms. However, the functional link between microbiota taxonomic compositions and disease suppression has not been explained yet. Here, we provide an overview of pathogen regulation in soil and mammals gut, highlighting the differences and the similarities between the two systems. First, we provide a review of the ecological mechanisms underlying the regulation of soil and pathogens, as well as the link between disease suppression and soil health. Particular emphasis is thus given to clarifying how soil and the gut microbiota are associated with organic amendment and the human diet, respectively. Moreover, we provide several insights into the importance of organic amendment and diet composition in shaping beneficial microbiota as an efficient way to support crop productivity and human health. This review also discusses novel ways to functionally characterize organic amendments and the proper operational combining of such materials with beneficial microbes for stirring suppressive microbiota against pathogens. Furthermore, specific examples are given to describe how agricultural management practices, including the use of antibiotics and fumigants, hinder disease suppression by disrupting microbiota structure, and the potentiality of entire microbiome transplant. We conclude by discussing general strategies to promote soil microbiota biodiversity, the connection with plant yield and health, and their possible integration through a “One Health” framework.

scholarly journals Factors Affecting Suppressiveness of Composts to Plant Diseases

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 749F-749
Author(s):  
H.A.J. Hoitink ◽  
A.G. Stone
Keyword(s):  
Plant Pathogens ◽  
Heat Exposure ◽  
Organic Amendments ◽  
Plant Diseases ◽  
Disease Suppression ◽  
Biocontrol Agents ◽  
Factors Affecting ◽  
Compost Stability ◽  
Commercial Scale ◽  
Treatment Conditions

Many factors affect the potential for composts to provide biological control of diseases caused by soilborne plant pathogens. Heat exposure during composting kills or inactivates pathogens and weed seeds if the process is monitored properly. Unfortunately, most beneficial microorganisms also are killed by this heat treatment. Conditions must be provided after peak heating that enhance natural recolonization of composts by biocontrol agents. The raw feedstock, the environment in which the compost is produced, as well as conditions during curing and utilization, determine the potential for recolonization by this microflora and the induction of disease suppression. Controlled inoculation of compost with biocontrol agents has proved necessary to induce consistent levels of suppression on a commercial scale. Compost stability is another important factor. Immature composts serve as food for pathogens and increase disease even when biocontrol agents are present. On the other hand, excessively stabilized organic amendments, such as highly decomposed peats, do not support the activity of biocontrol agents and disease therefore develops. Finally, salinity, C to N ratio, and other factors affect suppressiveness. Each of these factors will be discussed.

Assessing the sustainability of wheat-based cropping systems using APSIM: model parameterisation and evaluation

2007 ◽  
Vol 58 (1) ◽  
pp. 75 ◽  
Author(s):  
Carina Moeller ◽  
Mustafa Pala ◽  
Ahmad M. Manschadi ◽  
Holger Meinke ◽  
Joachim Sauerborn
Keyword(s):  
Organic Matter ◽  
Soil Water ◽  
Management Practices ◽  
Soil Depth ◽  
Crop Productivity ◽  
Water Dynamics ◽  
Soil Water Dynamics ◽  
Mineral N ◽  
N Use

Assessing the sustainability of crop and soil management practices in wheat-based rotations requires a well-tested model with the demonstrated ability to sensibly predict crop productivity and changes in the soil resource. The Agricultural Production Systems Simulator (APSIM) suite of models was parameterised and subsequently used to predict biomass production, yield, crop water and nitrogen (N) use, as well as long-term soil water and organic matter dynamics in wheat/chickpea systems at Tel Hadya, north-western Syria. The model satisfactorily simulated the productivity and water and N use of wheat and chickpea crops grown under different N and/or water supply levels in the 1998–99 and 1999–2000 experimental seasons. Analysis of soil-water dynamics showed that the 2-stage soil evaporation model in APSIM’s cascading water-balance module did not sufficiently explain the actual soil drying following crop harvest under conditions where unused water remained in the soil profile. This might have been related to evaporation from soil cracks in the montmorillonitic clay soil, a process not explicitly simulated by APSIM. Soil-water dynamics in wheat–fallow and wheat–chickpea rotations (1987–98) were nevertheless well simulated when the soil water content in 0–0.45 m soil depth was set to ‘air dry’ at the end of the growing season each year. The model satisfactorily simulated the amounts of NO3-N in the soil, whereas it underestimated the amounts of NH4-N. Ammonium fixation might be part of the soil mineral-N dynamics at the study site because montmorillonite is the major clay mineral. This process is not simulated by APSIM’s nitrogen module. APSIM was capable of predicting long-term trends (1985–98) in soil organic matter in wheat–fallow and wheat–chickpea rotations at Tel Hadya as reported in literature. Overall, results showed that the model is generic and mature enough to be extended to this set of environmental conditions and can therefore be applied to assess the sustainability of wheat–chickpea rotations at Tel Hadya.

scholarly journals The Significance of Bacillus spp. in Disease Suppression and Growth Promotion of Field and Vegetable Crops

2020 ◽  
Vol 8 (7) ◽  
pp. 1037 ◽  
Author(s):  
Dragana Miljaković ◽  
Jelena Marinković ◽  
Svetlana Balešević-Tubić
Keyword(s):  
Plant Growth ◽  
Plant Pathogens ◽  
Growth Promotion ◽  
Disease Suppression ◽  
Biocontrol Agents ◽  
Systemic Resistance ◽  
Steady Increase ◽  
Vegetable Crops ◽  
Wide Range ◽  
Bacillus Spp

Bacillus spp. produce a variety of compounds involved in the biocontrol of plant pathogens and promotion of plant growth, which makes them potential candidates for most agricultural and biotechnological applications. Bacilli exhibit antagonistic activity by excreting extracellular metabolites such as antibiotics, cell wall hydrolases, and siderophores. Additionally, Bacillus spp. improve plant response to pathogen attack by triggering induced systemic resistance (ISR). Besides being the most promising biocontrol agents, Bacillus spp. promote plant growth via nitrogen fixation, phosphate solubilization, and phytohormone production. Antagonistic and plant growth-promoting strains of Bacillus spp. might be useful in formulating new preparations. Numerous studies of a wide range of plant species revealed a steady increase in the number of Bacillus spp. identified as potential biocontrol agents and plant growth promoters. Among different mechanisms of action, it remains unclear which individual or combined traits could be used as predictors in the selection of the best strains for crop productivity improvement. Due to numerous factors that influence the successful application of Bacillus spp., it is necessary to understand how different strains function in biological control and plant growth promotion, and distinctly define the factors that contribute to their more efficient use in the field.

scholarly journals Modelling of long-term Zn, Cu, Cd and Pb dynamics from soils fertilised with organic amendments

SOIL ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 107-123
Author(s):  
Claudia Cagnarini ◽  
Stephen Lofts ◽  
Luigi Paolo D'Acqui ◽  
Jochen Mayer ◽  
Roman Grüter ◽  
...  
Keyword(s):  
Sewage Sludge ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Management Practices ◽  
Farmyard Manure ◽  
Organic Amendments ◽  
Mineral Weathering ◽  
Lateral Mixing ◽  
Critical Limits

Abstract. Soil contamination by trace elements (TEs) is a major concern for sustainable land management. A potential source of excessive inputs of TEs into agricultural soils are organic amendments. Here, we used dynamic simulations carried out with the Intermediate Dynamic Model for Metals (IDMM) to describe the observed trends of topsoil Zn (zinc), Cu (copper), Pb (lead) and Cd (cadmium) concentrations in a long-term (>60-year) crop trial in Switzerland, where soil plots have been treated with different organic amendments (farmyard manure, sewage sludge and compost). The observed ethylenediaminetetraacetic acid disodium salt (EDTA)-extractable concentrations ranged between 2.6 and 27.1 mg kg−1 for Zn, 4.9 and 29.0 mg kg−1 for Cu, 6.1–26.2 mg kg−1 for Pb, and 0.08 and 0.66 mg kg−1 for Cd. Metal input rates were initially estimated based on literature data. An additional, calibrated metal flux, tentatively attributed to mineral weathering, was necessary to fit the observed data. Dissolved organic carbon fluxes were estimated using a soil organic carbon model. The model adequately reproduced the EDTA-extractable (labile) concentrations when input rates were optimised and soil lateral mixing was invoked to account for the edge effect of mechanically ploughing the trial plots. The global average root mean square error (RMSE) was 2.7, and the average bias (overestimation) was −1.66, −2.18, −4.34 and −0.05 mg kg−1 for Zn, Cu, Pb and Cd, respectively. The calibrated model was used to project the long-term metal trends in field conditions (without soil lateral mixing), under stable climate and management practices, with soil organic carbon estimated by modelling and assumed trends in soil pH. Labile metal concentrations to 2100 were largely projected to remain near constant or to decline, except for some metals in plots receiving compost. Ecotoxicological thresholds (critical limits) were predicted to be exceeded presently under sewage sludge inputs and to remain so until 2100. Ecological risks were largely not indicated in the other plots, although some minor exceedances of critical limits were projected to occur for Zn before 2100. This study advances our understanding of TEs' long-term dynamics in agricultural fields, paving the way to quantitative applications of modelling at field scales.

Organic Amendments for Pathogen and Nematode Control

2020 ◽  
Vol 58 (1) ◽  
pp. 277-311 ◽  
Author(s):  
Erin Rosskopf ◽  
Francesco Di Gioia ◽  
Jason C. Hong ◽  
Cristina Pisani ◽  
Nancy Kokalis-Burelle
Keyword(s):  
Crop Production ◽  
Plant Pathogens ◽  
Production Systems ◽  
Organic Amendments ◽  
Molecular Techniques ◽  
Disease Suppression ◽  
Parasitic Nematodes ◽  
Vegetable Production ◽  
Significant Progress ◽  
Plant Parasitic

The loss of methyl bromide as a soil fumigant and minimal advances in the development and registration of new chemical fumigants has resulted in a resurgence of interest in the application of organic amendments (OAs) for soilborne plant pathogen and plant-parasitic nematode management. Significant progress has been made in the characterization of OAs, application of strategies for their use, and elucidation of mechanisms by which they suppress soilborne pests. Nonetheless, their utility is limited by the variability of disease control, expense, and the logistics of introducing them into crop production systems. Recent advances in molecular techniques have led to significant progress in the elucidation of the role of bacteria and fungi and their metabolic products on disease suppression with the addition of OAs. Biosolarization and anaerobic soil disinfestation, developed to manipulate systems and favor beneficial microorganisms to maximize their impact on plant pathogens, are built on a strong historical research foundation in OAs and the physical, chemical, and biological characteristics of disease-suppressive soils. This review focuses on recent applications of OAs and their potential for the management of soilborne plant pathogens and plant-parasitic nematodes, with emphasis primarily on annual fruit and vegetable production systems.

Soil carbon dynamics under different cropping and pasture management in temperate Australia: Results of three long-term experiments

Soil Research ◽  
2011 ◽  
Vol 49 (4) ◽  
pp. 320 ◽  
Author(s):  
K. Y. Chan ◽  
M. K. Conyers ◽  
G. D. Li ◽  
K. R. Helyar ◽  
G. Poile ◽  
...  
Keyword(s):  
Steady State ◽  
Management Practices ◽  
Agricultural Soils ◽  
Soil Depth ◽  
Crop Productivity ◽  
Wagga Wagga ◽  
Continuous Cropping ◽  
Pasture Management ◽  
The Impact

In addition to its important influence on soil quality and therefore crop productivity, soil organic carbon (SOC) has also been identified as a possible C sink for sequestering atmospheric carbon dioxide. Limited data are available on the impact of management practices on the rate of SOC change in agricultural soils in Australia. In this paper, results of three long-term trials (13–25 years) located near Wagga Wagga in temperate Australia were used to assess C dynamics under different tillage and stubble management practices, and under cropping intensities in pasture/crop rotations. Experimental results confirm the importance of management practices and pasture in determining first the steady-state SOC concentrations that are characteristic of given rotations and crop management systems, and second the rates of change of SOC concentrations as they approach steady-state concentrations in agricultural soils of this agro-ecological zone. A long-term crop/pasture experiment at a site with initial high SOC showed that the rate of SOC change in different treatments ranged from –278 to +257 kg C/ha.year over 0–0.3 m soil depth. Under continuous cropping, even under conservation agriculture practices of no-tillage, stubble retention, and crop rotation, the high initial SOC stock (0–0.3 m) present after a long-term pasture phase was, at best, maintained but tended to decrease with increased tillage or stubble burning practices. The effect of tillage was greater than that of stubble management. Increases in SOC were observed only in rotations incorporating a pasture phase. Our results suggest that improved soil nutrient and grazing management of permanent pasture can lead to an increase of 500–700 kg C/ha.year where the initial SOC concentrations are well below steady-state concentrations that could be expected after long periods of improved management. No difference was found between perennial pasture and annual pasture to the depth measured (0–0.3 m). Our results suggest that pasture holds the key to maintaining, and even increasing, SOC under crop/pasture in this environment.

scholarly journals Potato Growth and Yield Characteristics under Different Cropping System Management Strategies in Northeastern U.S.

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 165
Author(s):  
Robert P. Larkin ◽  
C. Wayne Honeycutt ◽  
Timothy S. Griffin ◽  
O. Modesto Olanya ◽  
Zhongqi He
Keyword(s):  
Cover Crops ◽  
Management Practices ◽  
Cropping Systems ◽  
Potato Crop ◽  
Organic Amendments ◽  
Cropping System ◽  
Crop Growth ◽  
Disease Suppression ◽  
Growth And Yield ◽  
Green Manures

Cropping systems and management practices that improve soil health may greatly enhance crop productivity. Four different potato cropping systems designed to address specific management goals of soil conservation (SC), soil improvement (SI), disease suppression (DS), and a status quo (SQ) standard rotation, along with a non-rotation (PP) control, were evaluated for their effects on potato crop growth, nutrient, and yield characteristics under both irrigated and non-irrigated (rainfed) conditions in field trials in Maine, USA, from 2004 to 2010. Both cropping system and irrigation significantly (p < 0.05) affected most potato crop parameters associated with growth and yield. All rotations increased tuber yield relative to the non-rotation PP control, and the SI system, which included yearly compost amendments, resulted in overall higher yields and a higher percentage of large-size tubers than all other systems with no irrigation (increases of 14 to 90%). DS, which contained disease-suppressive green manures and cover crops, produced the highest yields overall under irrigation (increases of 11 to 35%). Irrigation increased tuber yields in all cropping systems except SI (average increase of 27–37%). SI also resulted in significant increases in leaf area duration and chlorophyll content (as indicators of photosynthetic potential) and root and shoot biomass relative to other cropping systems, particularly under non-irrigated conditions. SI also resulted in higher shoot and tuber tissue concentrations of N, P, and K, but not most micronutrients. Overall, cropping systems that incorporate management practices such as increased rotation length and the use of cover crops, green manures, reduced tillage, and particularly, organic amendments, can substantially improve potato crop growth and yield. Irrigation also substantially increased growth and yield under normal field conditions in Maine, but SI, with its large organic amendments, was essentially a substitute for irrigation, producing comparable results without irrigation.

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